For me this works fine:
The Piratebay works without any cert warnings or other problems.
For IsoHunt the cert works, but Chromium displays a content warning in the URL bar, as some of the resources loaded by IsoHunt aren't encrypted. This isn't really a problem on Chromium, as there is no warning dialog. But maybe other browsers display a warning dialog instead.
Maybe the whole thing (SSL vs. non-SSL) should be a user-configurable option? E.g. some users will prefer to always use the SSL encrypted version, even if this means that there may be certificate warning.